In addition to 17 New Zealand track and road titles and eight World Cup track golds, Henderson has been New Zealand Track Cyclist of the Year (2001, 2002, 2003) and Athlete of the Year, Otago, New Zealand (2001, 2002, 2003).

Henderson left Team Sky at the end of 2011, and joined Lotto–Belisol, mainly to act as lead-out man for Andre Greipel.[11] He credited his success in this role to the positioning skills which he developed as a track rider, and having to compete against quicker road sprinters such as Greipel, Mark Cavendish and Marcel Kittel.[2] In April 2015, he expressed his opinion on Twitter that Fabio Aru of rival team Astana missed the Giro del Trentino not because of illness as it was announced, but because he had an ongoing investigation into his biological passport for doping. Henderson apologised shortly after.[12] He competed in the 2016 Tour de France.[13]

In August 2017 Henderson announced his retirement from competition, having competed in his last race, the 2017 Colorado Classic, and indicated that he would move into full-time coaching, having trained athletes since 2014.[2] The following month he was announced as Endurance Performance Director for USA Cycling.[1]